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| 2. |
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- 2019
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Journal article (peer-reviewed)
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| 3. |
- Correa, D. F., et al.
(author)
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Geographic patterns of tree dispersal modes in Amazonia and their ecological correlates
- 2023
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In: Global Ecology and Biogeography. - : Wiley. - 1466-822X .- 1466-8238. ; 32:1, s. 49-69
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Journal article (peer-reviewed)abstract
- Aim To investigate the geographic patterns and ecological correlates in the geographic distribution of the most common tree dispersal modes in Amazonia (endozoochory, synzoochory, anemochory and hydrochory). We examined if the proportional abundance of these dispersal modes could be explained by the availability of dispersal agents (disperser-availability hypothesis) and/or the availability of resources for constructing zoochorous fruits (resource-availability hypothesis). Time period Tree-inventory plots established between 1934 and 2019. Major taxa studied Trees with a diameter at breast height (DBH) >= 9.55 cm. Location Amazonia, here defined as the lowland rain forests of the Amazon River basin and the Guiana Shield. Methods We assigned dispersal modes to a total of 5433 species and morphospecies within 1877 tree-inventory plots across terra-firme, seasonally flooded, and permanently flooded forests. We investigated geographic patterns in the proportional abundance of dispersal modes. We performed an abundance-weighted mean pairwise distance (MPD) test and fit generalized linear models (GLMs) to explain the geographic distribution of dispersal modes. Results Anemochory was significantly, positively associated with mean annual wind speed, and hydrochory was significantly higher in flooded forests. Dispersal modes did not consistently show significant associations with the availability of resources for constructing zoochorous fruits. A lower dissimilarity in dispersal modes, resulting from a higher dominance of endozoochory, occurred in terra-firme forests (excluding podzols) compared to flooded forests. Main conclusions The disperser-availability hypothesis was well supported for abiotic dispersal modes (anemochory and hydrochory). The availability of resources for constructing zoochorous fruits seems an unlikely explanation for the distribution of dispersal modes in Amazonia. The association between frugivores and the proportional abundance of zoochory requires further research, as tree recruitment not only depends on dispersal vectors but also on conditions that favour or limit seedling recruitment across forest types.
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| 4. |
- Kattge, Jens, et al.
(author)
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TRY plant trait database - enhanced coverage and open access
- 2020
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In: Global Change Biology. - : Wiley-Blackwell. - 1354-1013 .- 1365-2486. ; 26:1, s. 119-188
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Journal article (peer-reviewed)abstract
- Plant traits-the morphological, anatomical, physiological, biochemical and phenological characteristics of plants-determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait-based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits-almost complete coverage for 'plant growth form'. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait-environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives.
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| 5. |
- Householder, John Ethan, et al.
(author)
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One sixth of Amazonian tree diversity is dependent on river floodplains
- 2024
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In: NATURE ECOLOGY & EVOLUTION. - 2397-334X.
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Journal article (peer-reviewed)abstract
- Amazonia's floodplain system is the largest and most biodiverse on Earth. Although forests are crucial to the ecological integrity of floodplains, our understanding of their species composition and how this may differ from surrounding forest types is still far too limited, particularly as changing inundation regimes begin to reshape floodplain tree communities and the critical ecosystem functions they underpin. Here we address this gap by taking a spatially explicit look at Amazonia-wide patterns of tree-species turnover and ecological specialization of the region's floodplain forests. We show that the majority of Amazonian tree species can inhabit floodplains, and about a sixth of Amazonian tree diversity is ecologically specialized on floodplains. The degree of specialization in floodplain communities is driven by regional flood patterns, with the most compositionally differentiated floodplain forests located centrally within the fluvial network and contingent on the most extraordinary flood magnitudes regionally. Our results provide a spatially explicit view of ecological specialization of floodplain forest communities and expose the need for whole-basin hydrological integrity to protect the Amazon's tree diversity and its function.
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| 6. |
- Luize, Bruno Garcia, et al.
(author)
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Geography and ecology shape the phylogenetic composition of Amazonian tree communities
- 2024
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In: JOURNAL OF BIOGEOGRAPHY. - 0305-0270 .- 1365-2699.
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Journal article (peer-reviewed)abstract
- Aim: Amazonia hosts more tree species from numerous evolutionary lineages, both young and ancient, than any other biogeographic region. Previous studies have shown that tree lineages colonized multiple edaphic environments and dispersed widely across Amazonia, leading to a hypothesis, which we test, that lineages should not be strongly associated with either geographic regions or edaphic forest types. Location: Amazonia. Taxon: Angiosperms (Magnoliids; Monocots; Eudicots). Methods: Data for the abundance of 5082 tree species in 1989 plots were combined with a mega-phylogeny. We applied evolutionary ordination to assess how phylogenetic composition varies across Amazonia. We used variation partitioning and Moran's eigenvector maps (MEM) to test and quantify the separate and joint contributions of spatial and environmental variables to explain the phylogenetic composition of plots. We tested the indicator value of lineages for geographic regions and edaphic forest types and mapped associations onto the phylogeny. Results: In the terra firme and v & aacute;rzea forest types, the phylogenetic composition varies by geographic region, but the igap & oacute; and white-sand forest types retain a unique evolutionary signature regardless of region. Overall, we find that soil chemistry, climate and topography explain 24% of the variation in phylogenetic composition, with 79% of that variation being spatially structured (R-2 = 19% overall for combined spatial/environmental effects). The phylogenetic composition also shows substantial spatial patterns not related to the environmental variables we quantified (R-2 = 28%). A greater number of lineages were significant indicators of geographic regions than forest types. Main Conclusion: Numerous tree lineages, including some ancient ones (>66 Ma), show strong associations with geographic regions and edaphic forest types of Amazonia. This shows that specialization in specific edaphic environments has played a long-standing role in the evolutionary assembly of Amazonian forests. Furthermore, many lineages, even those that have dispersed across Amazonia, dominate within a specific region, likely because of phylogenetically conserved niches for environmental conditions that are prevalent within regions.
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| 7. |
- ter Steege, Hans, et al.
(author)
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Mapping density, diversity and species-richness of the Amazon tree flora
- 2023
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In: COMMUNICATIONS BIOLOGY. - 2399-3642. ; 6:1
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Journal article (peer-reviewed)abstract
- Using 2.046 botanically-inventoried tree plots across the largest tropical forest on Earth, we mapped tree species-diversity and tree species-richness at 0.1-degree resolution, and investigated drivers for diversity and richness. Using only location, stratified by forest type, as predictor, our spatial model, to the best of our knowledge, provides the most accurate map of tree diversity in Amazonia to date, explaining approximately 70% of the tree diversity and species-richness. Large soil-forest combinations determine a significant percentage of the variation in tree species-richness and tree alpha-diversity in Amazonian forest-plots. We suggest that the size and fragmentation of these systems drive their large-scale diversity patterns and hence local diversity. A model not using location but cumulative water deficit, tree density, and temperature seasonality explains 47% of the tree species-richness in the terra-firme forest in Amazonia. Over large areas across Amazonia, residuals of this relationship are small and poorly spatially structured, suggesting that much of the residual variation may be local. The Guyana Shield area has consistently negative residuals, showing that this area has lower tree species-richness than expected by our models. We provide extensive plot meta-data, including tree density, tree alpha-diversity and tree species-richness results and gridded maps at 0.1-degree resolution. A study mapping the tree species richness in Amazonian forests shows that soil type exerts a strong effect on species richness, probably caused by the areas of these forest types. Cumulative water deficit, tree density and temperature seasonality affect species richness at a regional scale.
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| 8. |
- Rodrigues, Cândido C., et al.
(author)
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How do microplastics alter molluscicidal activity? Effects of weathered microplastics and niclosamide in developing freshwater snails
- 2024
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In: Science of the Total Environment. - : Elsevier BV. - 0048-9697 .- 1879-1026. ; 922
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Journal article (peer-reviewed)abstract
- Despite the wide distribution and persistence of microplastics (MPs), their interactive effects with molluscicides are unknown. Schistosomiasis, a neglected tropical disease, affects 236.6 million people worldwide. Niclosamide (NCL) is the only molluscicide recommended by the World Health Organization (WHO) and it is used to control the population of Schistosoma spp.'s intermediate host. Thus, this study aimed to evaluate of the interaction between polyethylene (PE) MPs and NCL, and their associated toxicity in the freshwater snail Biomphalaria glabrata (Say 1818). Weathered PE MPs were characterized and theoretical analysis of NCL-MP adsorption nature was made using quantum mechanical calculations. The toxicity of NCL isolated (0.0265 to 0.0809 mg L−1) and under interaction with PE MPs (3400 μg L−1) in B. glabrata embryos and newly hatched snails was analyzed. In silico analysis confirmed the adsorption mechanisms of NCL into PE MPs. PE MPs decreased the NCL toxicity to both B. glabrata developmental stages, increasing their survival and NCL lethal concentrations, indicating concerns regarding NCL use as molluscicide in aquatic environments polluted by MPs. In conclusion, MPs may change the efficiency of chemicals used in snail control programs.
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| 9. |
- Cooper, Declan L.M., et al.
(author)
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Consistent patterns of common species across tropical tree communities
- 2024
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In: Nature. - 0028-0836 .- 1476-4687. ; 625:7996, s. 728-734
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Journal article (peer-reviewed)abstract
- Trees structure the Earth’s most biodiverse ecosystem, tropical forests. The vast number of tree species presents a formidable challenge to understanding these forests, including their response to environmental change, as very little is known about most tropical tree species. A focus on the common species may circumvent this challenge. Here we investigate abundance patterns of common tree species using inventory data on 1,003,805 trees with trunk diameters of at least 10 cm across 1,568 locations 1–6 in closed-canopy, structurally intact old-growth tropical forests in Africa, Amazonia and Southeast Asia. We estimate that 2.2%, 2.2% and 2.3% of species comprise 50% of the tropical trees in these regions, respectively. Extrapolating across all closed-canopy tropical forests, we estimate that just 1,053 species comprise half of Earth’s 800 billion tropical trees with trunk diameters of at least 10 cm. Despite differing biogeographic, climatic and anthropogenic histories 7, we find notably consistent patterns of common species and species abundance distributions across the continents. This suggests that fundamental mechanisms of tree community assembly may apply to all tropical forests. Resampling analyses show that the most common species are likely to belong to a manageable list of known species, enabling targeted efforts to understand their ecology. Although they do not detract from the importance of rare species, our results open new opportunities to understand the world’s most diverse forests, including modelling their response to environmental change, by focusing on the common species that constitute the majority of their trees.
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| 10. |
- Olusegun, Sunday J., et al.
(author)
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Removal of doxorubicin hydrochloride and crystal violet from aqueous solutions using spray-dried niobium oxide coated with chitosan-activated carbon : Experimental and DFT calculations
- 2024
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In: International Journal of Biological Macromolecules. - : Elsevier BV. - 0141-8130 .- 1879-0003. ; 266
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Journal article (peer-reviewed)abstract
- Spray -dried niobium oxide coated with chitosan-activated carbon (NIC) was synthesized and used to remove doxorubicin hydrochloride and crystal violet from aqueous solutions under different parameters such as solution pH (2, 4, 6, and 8), contact time (1 to 9 h), initial concentration (20 to 200 mg L -1 ), and competing ions (0.1 M of CaCl 2 and NaCl). The addition of 5 % chitosan-activated carbon to the matrix of niobium oxide slightly increased the specific surface area from 26 to 30 m 2 g -1 , with the introduction of a carboxylic functional group. This led to an increase in the amount of adsorbed doxorubicin hydrochloride (DOH) from 30 to 44 mg g -1 and that of crystal violet (CV) from 15 to 32 mg g -1 from the initial respective 100 mg L -1 at pH 8. The data from the concentration study fitted into Liu isotherm having adsorption capacity of 128 and 57 mg g -1 for DOH and CV respectively, while pseudo first and second order are more suitable for adsorption kinetics. The additional functional groups on the IR spectrum of NIC after the adsorption of DOH and CV confirmed the interaction between NIC and the adsorbates' molecules. The mechanism of adsorption was supported by DFT calculations.
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| 11. |
- Diesen, Elias, et al.
(author)
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Accuracy of XAS theory for unraveling structural changes of adsorbates : CO on Ni(100)
- 2020
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In: AIP Advances. - : AIP Publishing. - 2158-3226. ; 10:11
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Journal article (peer-reviewed)abstract
- Studying surface reactions using ultrafast optical pump and x-ray probe experiments relies on accurate calculations of x-ray spectra of adsorbates for the correct identification of the spectral signatures and their dynamical evolution. We show that experimental x-ray absorption can be well reproduced for different binding sites in a static prototype system CO/Ni(100) at a standard density functional theory generalized-gradient-approximation level of theory using a plane-wave basis and pseudopotentials. This validates its utility in analyzing ultrafast x-ray probe experiments. The accuracy of computed relative core level binding energies is about 0.2 eV, representing a lower limit for which spectral features can be resolved with this method. We also show that the commonly used Z + 1 approximation gives very good core binding energy shifts overall. However, we find a discrepancy for CO adsorbed in the hollow site, which we assign to the significantly stronger hybridization in hollow bonding than in on-top.
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| 12. |
- Lömker, Patrick, et al.
(author)
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Operando XPS and SXRD study of the Fischer-Tropsch reaction on flat and stepped Co at up to around 1 bar
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Other publication (other academic/artistic)abstract
- The Fischer-Tropsch catalytic reaction on Co has still several unknows regarding the surface chemical state of the catalyst and presence of various adsorbed intermediates appearing under operando conditions. Here, we report an operando X-ray photoelectron spectroscopy study of the flat Co(0001) and stepped Co(10-14) model catalyst surfaces during Fischer-Tropsch synthesis conditions at 150 mbar – 975 mbar pressure and 406 K – 548 K temperature in a H2/CO gas mixture using X-ray photoelectron spectroscopy as well surface X-ray diffraction. We observe that the Co surface remains metallic at all conditions with only adsorbed species. There are a number of different intermediates on the surface such as adsorbed CO in only on-top position, C/-CH intermediates, -CH2- species and various longer hydrocarbon molecules. The coverage of the hydrocarbon species decreases with increasing temperature but increase strongly with pressure. The stepped surface shows a significant increase in adsorbed hydrocarbon species which is a clear indication of higher reactivity. There is no observation of any CHO or CH2O species indicating a direct CO dissociation pathway and that to our observation only hydrocarbon species participate in the chain growth. The relative high coverage of CO that is almost constant for the various conditions points to that CO dissociation is one of the rate-limiting steps. The rapid increase in the coverage of hydrocarbon species at high pressure conditions and on the stepped surface further indicates that the final hydrogen induced termination step is also rate-limiting. By following the time dependence of the C 1s region with rapid change in the flow of reactants, we demonstrate that the surface species are highly dynamic resulting in delays in reaching steady-state conditions.
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| 13. |
- Olusegun, Sunday J., et al.
(author)
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Comparative characteristics and enhanced removal of tetracycline and ceftriaxone by Fe3O4-lignin and Fe3O4-carbon-based lignin : Mechanism, thermodynamic evaluation, and DFT calculation
- 2023
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In: Journal of Molecular Liquids. - : Elsevier BV. - 0167-7322 .- 1873-3166. ; 371
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Journal article (peer-reviewed)abstract
- In this study, eco-friendly Fe3O4-lignin (FeL) and Fe3O4-carbon-based lignin (FeCL) were synthesized, characterized, and applied for the adsorption of tetracycline (TRC) and ceftriaxone (CEF). Comparative characterization showed that the BET-specific surface area of FeCL is 27 m2/g more than that of FeL. The difference in their morphologies is insignificant, and the particle sizes range between 5 and 15 nm. There is a reduction in the oxygen content and hydroxyl group of FeCL as shown from the EDS and FTIR spectra respectively, compared with FeL. The adsorption capacity for the removal of TRC at 333 K is 156 and 148 mg g-1 by FeL and FeCL, respectively; while that of CEF are virtually the same. FeL and FeCL adsorption capacity for TRC increases with temperatures (endothermic), but decreases (exothermic) for CEF. The combination of experimental and computational approaches gave insight into the mechanisms of the adsorption process. The mechanisms of TRC and CEF adsorption by FeL and FeCL are the electrostatic attraction, hydrophobic, and 7C -7C interaction, while only FeL shows the possibility of hydrogen bond with both TRC and CEF. The study demonstrated that the synthesized material can be reused for up to 3 cycles without an alarming loss of efficiency capacity.
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| 14. |
- Rodrigues, Gabriel L. S., et al.
(author)
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Multiconfigurational pair-density functional theory is more complex than you may think
- 2023
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In: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 127:44, s. 9381-9388
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Journal article (peer-reviewed)abstract
- Multiconfigurational pair-density functional theory (MC-PDFT) is a promising way to describe both strong and dynamic correlations in an inexpensive way. The functionals in MC-PDFT are often “translated” from standard spin density functionals. However, these translated functionals can in principle lead to “translated spin densities” with a nonzero imaginary component. Current developments so far neglect this imaginary part by simply setting it to zero. In this work, we show how this imaginary component is actually needed to reproduce the correct physical behavior in a range of cases, especially low-spin open shells. We showcase the resulting formalism on both local density approximation and generalized gradient approximation functionals and illustrate the numerical behavior by benchmarking a number of singlet-triplet splittings (ST gaps) of organic diradicals and low-lying excited states of some common organic molecules. The results demonstrate that this scheme improves existing translated functionals and gives more accurate results, even with minimal active spaces.
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| 15. |
- Scott, Mikael, et al.
(author)
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Variational Pair-Density Functional Theory : Dealing with Strong Correlation at the Protein Scale
- 2024
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In: Journal of Chemical Theory and Computation. - 1549-9618. ; 20:6
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Journal article (peer-reviewed)abstract
- Multiconfigurational pair-density functional theory (MC-PDFT) offers a promising solution to the challenges faced by traditional density functional theory (DFT) in addressing molecular systems containing transition metals, open-shells, or strong correlations in general. By utilizing both the density and on-top pair-density, MC-PDFT can make use of a more flexible multiconfigurational wave function to capture the necessary static correlation, while the pair-density functional also includes the effect of dynamic correlation. So far, MC-PDFT has been used after a multiconfigurational self-consistent field (MCSCF) step, using the orbitals and configuration interaction coefficients from the converged MCSCF wave function to compute PDFT energies and properties. Here, instead, we propose to perform a direct optimization of the wave function using the pair-density functionals, resulting in a variational formulation of MC-PDFT. We derive the expressions for the wave function gradient and illustrate their similarity to standard MCSCF equations. Furthermore, we illustrate the accuracy on a set of singlet-triplet gaps as well as dissociation curves. Our findings highlight one of MC-PDFT’s standout features: a reduced dependency on the active space size compared to conventional multiconfigurational wave function methodologies. Additionally, we show that the computational cost of MC-PDFT is potentially lower than MCSCF and often on-par with standard Kohn-Sham DFT, which is demonstrated by performing a MC-PDFT calculation of the entire ferredoxin protein with 1447 atoms and nearly 12 000 basis functions.
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| 16. |
- Shipilin, Mikhail, et al.
(author)
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In Situ Surface-Sensitive Investigation of Multiple Carbon Phases on Fe(110) in the Fischer-Tropsch Synthesis
- 2022
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In: ACS Catalysis. - : American Chemical Society (ACS). - 2155-5435. ; 12:13, s. 7609-7621
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Journal article (peer-reviewed)abstract
- Carbide formation on iron-based catalysts is an integral and, arguably, the most important part of the Fischer–Tropsch synthesis process, converting CO and H2 into synthetic fuels and numerous valuable chemicals. Here, we report an in situ surface-sensitive study of the effect of pressure, temperature, time, and gas feed composition on the growth dynamics of two distinct iron–carbon phases with the octahedral and trigonal prismatic coordination of carbon sites on an Fe(110) single crystal acting as a model catalyst. Using a combination of state-of-the-art X-ray photoelectron spectroscopy at an unprecedentedly high pressure, high-energy surface X-ray diffraction, mass spectrometry, and theoretical calculations, we reveal the details of iron surface carburization and product formation under semirealistic conditions. We provide a detailed insight into the state of the catalyst’s surface in relation to the reaction.
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| 17. |
- Valter-Lithander, Mikael, et al.
(author)
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Microkinetic Model Fitted with a Genetic Algorithm to Experimental XPS Coverages at High Pressure-CO Hydrogenation on Rh(111)
- 2024
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In: Journal of Physical Chemistry C. - 1932-7447 .- 1932-7455. ; 128:28, s. 11598-11611
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Journal article (peer-reviewed)abstract
- Comparisons to experiments are important when developing kinetic models based on density functional theory (DFT) calculations. The comparisons are, however, often challenging due to the assumed uncertainties in the energies from which the kinetic parameters are calculated. Here, we introduce a genetic algorithm to adjust the DFT-energies to better match experimental XPS data, using CO hydrogenation on Rh(111) as an example. The adjustments are made to adsorption energies, adsorbate-adsorbate interactions, XPS energies, and peak shapes. While these parameters improve the experimental agreement considerably, the required changes to the DFT energies are relatively large, which indicates the need for refined treatments of, for example, possible surface species and reaction steps, surface inhomogeneities, or higher levels of electronic structure calculations. We propose the genetic-algorithm based method as a general tool for assessment of computational models.
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